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BIOLOGICAL SCIENCE
FOURTH EDITION
SCOTT FREEMAN
Lectures by Stephanie Scher Pandolfi
2011 Pearson Education, Inc.
Key Concepts
Most cell functions depend on proteins. Proteins are made of amino acids. Amino acids vary in structure and function. The structure of a protein can be analyzed at four levels: 1. Amino acid sequence 2. Substructures called -helices and -pleated sheets 3. Interactions between amino acids that dictate a proteins overall shape 4. Combinations of individual proteins that make up larger, multiunit molecules In cells, most proteins are enzymes that function as catalysts.
2011 Pearson Education, Inc.
1. Production of small organic compounds i.e., formaldehyde (H2CO), hydrogen cyanide (HCN) 2. Formation of mid-sized molecules from these small compounds i.e., amino acids, simple sugars These molecules combined with ocean water to form prebiotic soup. 3. Mid-sized building blocks combine to form large molecules. i.e., proteins, complex carbohydrates 4. Life became possible when one of these large molecules selfreplicated.
2011 Pearson Education, Inc.
To find out, Stanley Miller combined methane (CH4), ammonia (NH3), and hydrogen (H2) in a closed system with water, and applied heat and electricity as an energy source. The products included hydrogen cyanide (HCN) and formaldehyde (H2CO), important precursors for more-complex organic molecules and amino acids.
In more recent experiments, amino acids and other organic molecules have been found to form easily under these conditions.
2011 Pearson Education, Inc.
Amino acids with hydroxyl, amino, carboxyl, or sulfhydryl functional groups in their side chains are more chemically reactive than those with side chains composed of only carbon and hydrogen atoms.
Macromolecules are very large polymers made up of many monomers linked together.
Thus, proteins are macromolecules consisting of linked amino acid monomers.
Building Proteins
Polypeptide Characteristics
Within the polypeptide, the peptide bonds form a backbone with three key characteristics:
1. R-group orientation Side chains can interact with each other or water. 2. Directionality Free amino group, on the left, is called the N-terminus. Free carboxyl group, on the right, is called the Cterminus. 3. Flexibility Single bonds on either side of the peptide bond can rotate, making the entire structure flexible.
Primary Structure
A proteins primary structure is its unique sequence of amino acids. Because the amino acid R-groups affect a polypeptides properties and function, just a single amino acid change can radically alter protein function.
Glu 6
Glu 7
Val 6
Glu 7
Secondary Structure
Hydrogen bonds between the carbonyl group of one amino acid and the amino group of another form a proteins secondary structure. A polypeptide must bend to allow this hydrogen bonding, forming: -helices -pleated sheets
Secondary structure depends on the primary structure. Some amino acids are more likely to be involved in -helices; others, in -pleated sheets. The large number of hydrogen bonds in a proteins secondary structure increases its stability.
2011 Pearson Education, Inc.
Tertiary Structure
The tertiary structure of a polypeptide results from interactions between R-groups or between R-groups and the peptide backbone. These contacts cause the backbone to bend and fold, and contribute to the distinctive three-dimensional shape of the polypeptide. R-group interactions include hydrogen bonds, hydrophobic interactions, van der Waals interactions, covalent disulfide bonds, and ionic bonds.
Quaternary Structure
Many proteins contain several distinct polypeptide subunits that interact to form a single structure; the bonding of two or more subunits produces quaternary structure.
Prions can induce normal protein molecules to change their shape to the altered form.
An Introduction to Catalysis
Catalysis may be the most fundamental of protein functions. Reactions take place when: Reactants collide in precise orientation Reactants have enough kinetic energy to overcome repulsion between the electrons that come in contact during bond formation Enzymes perform two functions: 1. Bring substrates together in precise orientation so that the electrons involved in the reaction can interact 2. Decrease the amount of kinetic energy reactants must have for the reaction to proceed
2011 Pearson Education, Inc.
Catalysts lower the activation energy of a reaction by lowering the free energy of the transition state.
Catalysts do not change G and are not consumed in the reaction.
Enzymes
Enzymes are protein catalysts and typically catalyze only one reaction. Most biological chemical reactions occur at meaningful rates only in the presence of an enzyme. Enzymes: 1. Bring reactants together in precise orientations 2. Stabilize transition states Protein catalysts are important because they speed up the chemical reactions that are required for life.
Enzyme Regulation
Competitive inhibition occurs when a molecule similar in size and shape to the substrate competes with the substrate for access to the active site. Allosteric regulation occurs when a molecule causes a change in enzyme shape by binding to the enzyme at a location other than the active site. Allosteric regulation can activate or deactivate the enzyme.
1. Amino acids were abundant in the prebiotic soup. 2. Proteins are the most efficient catalysts known. 3. A self-replicating molecule had to act as a catalyst for the assembly and polymerization of its copy.
However, the first self-replicator probably needed to have a mold or a templatesomething not found in proteins.